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Medical Forum / Diseases and Disorders / AIDS / August 2008

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ISAC Congress Data Standards Committee a Purdue University Cytometry     Labatory Mail List Discussion

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Mitch Haynes - 30 Jul 2008 05:22 GMT
Reformating FCS to meet specific clincal needs is a bit self centered
for
>>those requesting that this be done. Those who have full time programmers
>>or those that sell products for data analysis are needed to help users,
>>not to dictate what they  need.
>>Jim Houston

From: Robert C. Leif, Ph.D. (rl...@rleif.com)
Date: Tue Jul 29 1997 - 20:25:22 EST
*       Next message: Vincent Falco: "Salary Survey Responses"
*       Previous message: Maryalice Stetler-Stevenson: "Re: CD20
Gating"
*       Maybe in reply to: Jim Houston: "Re: Re[2]: Leave FCS3.0
alone."
*       Next in thread: Dave Coder: "Re: Re[2]: Is FCS3.0 obsolete?"
*       Messages sorted by: [ date ] [ thread ] [ subject ]
[ author ]
[ attachment ]
________________________________________
To: cyto-inbox
From: Bob Leif

Please see Suzanne Leif's and my posting on the ISAC web site and
R. C. Leif and S. B. Leif, "Evolution of Flow Cytometry Standard,
FCS3.0,
into a DICOM-Compatible Format". Optical Diagnostics of Biological
Fluids
and Advanced Techniques in Analytical Cytology, Ed. A. V. Priezzhev ,
T.
Asakura, and R. C. Leif. A. Katzir Series Editor, Progress Biomedical
Optics Series , SPIE Proceedings Series,Vol. 2982, pp 354-366 (1997).

Many of your very good suggestions were separately arrived at by us.
However, there are two separate subjects: 1) What should be included
in a
Flow Cytometry File for Data Transfer and 2) The actual format for
the
Flow
Cytometry File for Data Transfer.  We suggested switching to the
Digital
Imaging and Communications in Medicine, DICOM, format after the year
2000.

My client Phoenix Flow has a product, QC-Tracker, which can be
transformed
into a generic FCS reader, data storage system, and user programmable
data
analysis system.  Would you or others be interested in this type of
product?
---------------------------------------------------------------------------­-
---------------------------------
At 03:35 PM 7/28/97 +0100, you wrote:

>As one of Jim Houston's "backyard" flow people (I actually do have a
>FACStar plus in my backyard- see advert in another message) who dabbles
>with programming, I would like to see a little less flexibility, and more
>standardisation in the standard. I believe that integer-based data files
>are the way to go, losing the ascii and floating point options (which I
>haven't seen implemented).  I would also lose the multiple data-set file
>option, since this could be better handled by a separate database manager,
>or even by putting a group of files in a separate directory. I would
>implement a record/structure -based text section with only the mandatory
>keywords and their values (this could be made backwards-compatible by
>including the old delimiters) to overcome misinterpretation of the text
>section format by those implementing FCS software, and allowing readers to
>parse through errors (such as empty value fields) more readily; at the very
>least I'd make a standard delimiter.  It would also speed things up parsing
>wise if there were three file types, one for each data mode with file type
>flagged in the header: eg FCS3.U, FCS3.C, FCS3.L for histogram, contour,
>and list data respectively, notice that this alternative naming wouldn't
>change the string length for the file type information, and if there is
>ever a revision of FCS 3, the fifth character could be used to denote it.
>Since the data are organised so differently in each of these types, and
>they are handled so differently, I think it's reasonable that these
>differences are flagged early in the parsing.
>I would put user-specified keywords in a section separate from the (now)
>structured text section, the analysis section would be ideal.
>The advantages of the above changes are that they are compatible with the
>proposed standard, but speed up and ease parsing (and writing) of the
>information that are needed to properly analyse the file.  Using a
>structured text section removes ambiguity caused by a commentable delimiter
>(eg cytomation's empty values, BD's LYSYS allowing you type the delimiter
>into text fields).  User-specific data would be written to a different
>section (the analysis part), where it can be found by those in the know.
>To avoid Swiftian confusion over byte order it may be worthwhile explicitly
>writing an integer constant (eg 1) into the text part, this would allow
>automatic detection of byte order, since if byte swapped it would be read
>incorrectly (eg as 256), an integer based on printable character values
>might be preffered.
>Mario roederer's wish list hasn't hit the forum yet, so it looks like this
>list  may be the the easiest place for these discussions, that's why I've
>sent my message here, and it's where I'd prefer to see the discussion held.
>Ray

>(ME!ME!ME!- sorry about the egocentric nature of this letter)

>At 12:24 pm -0500 18/7/97, Jim Houston wrote:

>>I would like to see FCS3.0 left alone.  There are many users in Flow who
>>have no idea what the capablilities of the FCS standard are or what it
>>does for them.

>>I have seen the world of flow data stored differently by each vendor.

Let

>>us not go back to that. FCS has served the flow world well.

>>Let us also not forget the backyard flow persons who dabble at programming
>>on their spare time to make FCS work for them. Who share code and ideas.
From: Robert C. Leif, Ph.D. (rl...@rleif.com)
Date: Tue Jul 29 1997 - 20:25:22 EST
*       Next message: Vincent Falco: "Salary Survey Responses"
*       Previous message: Maryalice Stetler-Stevenson: "Re: CD20
Gating"
*       Maybe in reply to: Jim Houston: "Re: Re[2]: Leave FCS3.0
alone."
*       Next in thread: Dave Coder: "Re: Re[2]: Is FCS3.0 obsolete?"
*       Messages sorted by: [ date ] [ thread ] [ subject ]
[ author ]
[ attachment ]
________________________________________
To: cyto-inbox
From: Bob Leif

Please see Suzanne Leif's and my posting on the ISAC web site and
R. C. Leif and S. B. Leif, "Evolution of Flow Cytometry Standard,
FCS3.0,
into a DICOM-Compatible Format". Optical Diagnostics of Biological
Fluids
and Advanced Techniques in Analytical Cytology, Ed. A. V. Priezzhev ,
T.
Asakura, and R. C. Leif. A. Katzir Series Editor, Progress Biomedical
Optics Series , SPIE Proceedings Series,Vol. 2982, pp 354-366 (1997).

Many of your very good suggestions were separately arrived at by us.
However, there are two separate subjects: 1) What should be included
in a
Flow Cytometry File for Data Transfer and 2) The actual format for
the
Flow
Cytometry File for Data Transfer.  We suggested switching to the
Digital
Imaging and Communications in Medicine, DICOM, format after the year
2000.

My client Phoenix Flow has a product, QC-Tracker, which can be
transformed
into a generic FCS reader, data storage system, and user programmable
data
analysis system.  Would you or others be interested in this type of
product?
---------------------------------------------------------------------------­-
---------------------------------
At 03:35 PM 7/28/97 +0100, you wrote:

>As one of Jim Houston's "backyard" flow people (I actually do have a
>FACStar plus in my backyard- see advert in another message) who dabbles
>with programming, I would like to see a little less flexibility, and more
>standardisation in the standard. I believe that integer-based data files
>are the way to go, losing the ascii and floating point options (which I
>haven't seen implemented).  I would also lose the multiple data-set file
>option, since this could be better handled by a separate database manager,
>or even by putting a group of files in a separate directory. I would
>implement a record/structure -based text section with only the mandatory
>keywords and their values (this could be made backwards-compatible by
>including the old delimiters) to overcome misinterpretation of the text
>section format by those implementing FCS software, and allowing readers to
>parse through errors (such as empty value fields) more readily; at the very
>least I'd make a standard delimiter.  It would also speed things up parsing
>wise if there were three file types, one for each data mode with file type
>flagged in the header: eg FCS3.U, FCS3.C, FCS3.L for histogram, contour,
>and list data respectively, notice that this alternative naming wouldn't
>change the string length for the file type information, and if there is
>ever a revision of FCS 3, the fifth character could be used to denote it.
>Since the data are organised so differently in each of these types, and
>they are handled so differently, I think it's reasonable that these
>differences are flagged early in the parsing.
>I would put user-specified keywords in a section separate from the (now)
>structured text section, the analysis section would be ideal.
>The advantages of the above changes are that they are compatible with the
>proposed standard, but speed up and ease parsing (and writing) of the
>information that are needed to properly analyse the file.  Using a
>structured text section removes ambiguity caused by a commentable delimiter

>(eg cytomation's empty values, BD's LYSYS allowing you type the delimiter
>into text fields).  User-specific data would be written to a different
>section (the analysis part), where it can be found by those in the know.
>To avoid Swiftian confusion over byte order it may be worthwhile explicitly
>writing an integer constant (eg 1) into the text part, this would allow
>automatic detection of byte order, since if byte swapped it would be read
>incorrectly (eg as 256), an integer based on printable character values
>might be preffered.

>Mario roederer's wish list hasn't hit the forum yet, so it looks like this
>list  may be the the easiest place for these discussions, that's why I've
>sent my message here, and it's where I'd prefer to see the discussion held.
>Ray

>(ME!ME!ME!- sorry about the egocentric nature of this letter)

>At 12:24 pm -0500 18/7/97, Jim Houston wrote:
>>I would like to see FCS3.0 left alone.  There are many users in Flow who
>>have no idea what the capablilities of the FCS standard are or what it
>>does for them.
>>I have seen the world of flow data stored differently by each vendor.  Let
>>us not go back to that. FCS has served the flow world well.
>>Let us also not forget the backyard flow persons who dabble at programming
>>on their spare time to make FCS work for them. Who share code and ideas.
>>Reformating FCS to meet specific clincal needs is a bit self centered for
>>those requesting that this be done. Those who have full time programmers
>>or those that sell products for data analysis are needed to help users,
>>not to dictate what they  need.
>>Jim Houston
>                              Ray Hicks
>________________________________________________________________________
>|University of Cambridge          |Tel              01223 330149        |
>|Department of Medicine           |Fax             01223 336846         |
>|Level 5, Addenbrookes Hospital   |e-mail         <rh...@cus.cam.ac.uk> |
>|Hills Road Cambridge             |Web  http://facsmac.med.cam.ac.uk    |
>|CB2                              |ftp server  ftp://131.111.80.78      |
>|UK                               |                                     |
>|_________________________________|_____________________________________|

________________________________________
*       Next message: Vincent Falco: "Salary Survey Responses"

>                              Ray Hicks
>________________________________________________________________________
>|University of Cambridge          |Tel              01223 330149        |
>|Department of Medicine           |Fax             01223 336846         |
>|Level 5, Addenbrookes Hospital   |e-mail         <rh...@cus.cam.ac.uk> |
>|Hills Road Cambridge             |Web  http://facsmac.med.cam.ac.uk    |
>|CB2                              |ftp server  ftp://131.111.80.78      |
>|UK                               |                                     |
>|_________________________________|_____________________________________|

________________________________________
*       Next message: Vincent Falco: "Salary Survey Responses"

Purdue Cytometry Mail List Plans to have Isac Congress Persuade the
FDA to FORCE their FCS STANDARDS!

From: Randy T. Fischer (fisch...@vax.grc.nia.nih.gov) Date: Thu Jul 17
1997 - 03:25:15 EST * Next message: kc...@samsung.co.kr: "LDL Receptor
Assay for FH" * Previous message: Bob Ashcroft: "RE: Cell Culture
after DNA Ploidy Staining" * Messages sorted by: [ date ] [ thread ]
[ subject ] [ author ] [ attachment ]
________________________________________ I agree with both Marty and
Gunter in the very important issue of standardizing data formatting. I
would point out that lobbying ISAC is only, however, part of the
answer. Regardless of what ISAC may choose to recommend, it is still
up to the manufacturers to implement what they want to do, and if they
do not agree with ISAC, then too bad for ISAC and the flow community.
A potentially more powerful force for change might be the FDA, which
regulates machines used in CLINICAL settings.

If the FDA could be persuaded to require all CLINICAL data be
universally both accessible and readable, then the manufacurers would
be forced to upgrade machines and software

or

lose theLUCRATIVE CLINICAL market.

This would make anlyzing data from different sources easier, and could
facilitate the exchange of crucial clinical results from various
trials where multiple sites and machines are in use.

So how does this get done?

Gunter (and Paul's agreeing response) are correct this needs to be
revisited at Asilomar, with perhaps an additional idea.

Any concrete standardization protocol, FCS3.0 or whatever it ends up
being designated, should be then presented to any and all regulatory
agencies by ISAC to ensure no individual manufacturer decides FCS3.0
in their format is acceptable, even if it is not universally
readable.

Randy T. Fischer NIA/NIH GRC Baltimore, MD 21224
fisch...@vax.grc.nia.nih.gov

Is this Collusion on the Purdue Cytometry Mail List Would the Purdue
Cytoemtry Mail List Software Vendors and the President of ISAC J Paul
Robinson Fall into a the definition of COLLUSION? KEEPING OTHER
VENDORS FROM ENTERING THE MARKET SINCE THE PURDUE CYTOMETRY MAIL LIST
IS THE ONLY OUTLET WITH ISAC AND EVERY UNIVERSITY..ECT
Collusion is an agreement, usually secretive, which occurs between two
or more persons to deceive, mislead, or defraud others of legal
rights, or to obtain an objective forbidden by law typically involving
fraud or gaining an unfair advantage and can involve "wage fixing,
kickbacks, or misrepresenting the independence of the relationship
between the colluding parties."[1] All acts affected by collusion are
considered void.[2]
http://en.wikipedia.org/wiki/Collusion

http://yedda.com/questions/Collusion_Purdue_Cytometry_Mail_2730616624105/
Mitch Haynes - 04 Aug 2008 18:27 GMT
> Reformating FCS to meet specific clincal needs is a bit self centered
> for
[quoted text clipped - 290 lines]
>
> - Show quoted text -

http://groups.google.com/group/misc.health.aids/browse_thread/thread/680ff619df929e95

USE THE LINK ABOVE SOME HOW SOME ONE IS HAVING ALL MY Yedda questions
deleted one more for the Collusion Idea. Pluss all my Yahoo Questions
too
Mitch Haynes - 04 Aug 2008 22:08 GMT
> Reformating FCS to meet specific clincal needs is a bit self centered
> for
[quoted text clipped - 292 lines]
> considered void.[2]
> http://en.wikipedia.org/wiki/Collusion

http://groups.google.ms/group/misc.health.aids/browse_thread/thread/76c3804aae39d1a6#
Mitch Haynes - 04 Aug 2008 22:08 GMT
> Reformating FCS to meet specific clincal needs is a bit self centered
> for
[quoted text clipped - 286 lines]
>
> http://yedda.com/questions/Collusion_Purdue_Cytometry_Mail_2730616624...

http://groups.google.ms/group/misc.health.aids/browse_thread/thread/76c3804aae39d1a6#
Mitch Haynes - 27 Aug 2008 23:48 GMT
> Reformating FCS to meet specific clincal needs is a bit self centered
> for
[quoted text clipped - 286 lines]
>
> http://yedda.com/questions/Collusion_Purdue_Cytometry_Mail_2730616624...

THE 24 PAGES OF COLLUSION POSTINGS WAS DELETED NOW THEY HAVE BEEN
POSTED ON MY FACEBOOK.

17 YEARS OF ARCHIVES NOW OVER 450 POSTING AND GROWING EVERY DAY.

IT TAKES AWHILE TO POST THE BEST OUT OF 17YEARS!

NOW YOUR DATA STANDARDS COMMITTEE AND LEADING SOFTWARE DEVELOPERS!

http://www.facebook.com/note.php?note_id=23879772873&ref=mf

http://www.facebook.com/note.php?note_id=23879772873&ref=mf

http://www.facebook.com/note.php?note_id=23879772873&ref=mf
Mitch Haynes - 27 Aug 2008 23:49 GMT
> Reformating FCS to meet specific clincal needs is a bit self centered
> for
[quoted text clipped - 286 lines]
>
> http://yedda.com/questions/Collusion_Purdue_Cytometry_Mail_2730616624...

http://www.facebook.com/note.php?note_id=23879772873&ref=mf
http://www.facebook.com/note.php?note_id=23879772873&ref=mf
http://www.facebook.com/note.php?note_id=23879772873&ref=mf
 
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